FTR, the premature thing is only in the novel. The timeframe of her relationship with Richard is not established in the movie. I'm not sure when they became involved - the prequel comic timeline doesn't make sense to me, and I think it's one of Singer's attempts to throw us off. Personally, right now I'm going with both Richard and Lois knowing Jason isn't Richard's (as well as the DP folks knowing that) and that they became involved later in her pregnancy or when Jason was very, very young (fans are debating this). But he's still the only father Jason has ever known.
But hey, the sequel could prove me wrong.
I have large issues with the timeframe anyway, just on Jason's age and how long Superman has been gone for.